Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori

Transcriptome analysis provides new insight into the mechanism of Bombyx mori under zinc exposure

Zinc is a significant source of heavy metal pollution that poses risks to both human health and biodiversity. Excessive concentrations of zinc can hinder the growth and development of insects and trigger cell death through oxidative damage. The midgut is the main organ affected by exposure to heavy metals. The silkworm, a prominent insect species belonging to the Lepidoptera class and widely used in China, serves as a model for studying the genetic response to heavy metal stress. In this study, high-throughput sequencing technology was employed to investigate detoxification-related genes in the midgut that are induced by zinc exposure. A total of 11,320 unigenes and 14,723 transcripts were identified, with 553 differentially expressed genes (DEGs) detected, among which 394 were up-regulated and 159 were down-regulated. The Gene Ontology (GO) analysis revealed that 452 DEGs were involved in 18 biological process subclasses, 14 cellular component subclasses and 8 molecular functional subclasses. Furthermore, the KEGG analysis demonstrated enrichment in pathways such as Protein digestion, absorption and Lysosome. Validation of the expression levels of 9 detoxification-related DEGs through qRT-PCR confirmed the accuracy of the RNA-seq results. This study not only contributes new insights into the detoxification mechanisms mechanism of silkworms against zinc contamination, but also serves as a foundation basis for understanding the molecular detoxification processes in lepidopteran insects.

Transcriptome Analysis Reveals Antioxidant Defense Mechanisms in the Silkworm Bombyx mori after Exposure to Lead

Lead (Pb) is a major source of heavy metal contamination, and poses a threat to biodiversity and human health. Elevated levels of Pb can hinder insect growth and development, leading to apoptosis via mechanisms like oxidative damage. The midgut of silkworms is the main organ exposed to heavy metals. As an economically important lepidopteran model insect in China, heavy metal-induced stress on silkworms causes considerable losses in sericulture, thereby causing substantial economic damage. This study aimed to investigate Pb-induced detoxification-related genes in the midgut of silkworms using high-throughput sequencing methods to achieve a deeper comprehension of the genes' reactions to lead exposure. This study identified 11,567 unigenes and 14,978 transcripts. A total of 1265 differentially expressed genes (DEGs) were screened, comprising 907 upregulated and 358 downregulated genes. Subsequently, Gene Ontology (GO) classification analysis revealed that the 1265 DEGs were distributed across biological processes, cellular components, and molecular functions. This suggests that the silkworm midgut may affect various organelle functions and biological processes, providing crucial clues for further exploration of DEG function. Additionally, the expression levels of 12 selected detoxification-related DEGs were validated using qRT-PCR, which confirmed the reliability of the RNA-seq results. This study not only provides new insights into the detoxification defense mechanisms of silkworms after Pb exposure, but also establishes a valuable foundation for further investigation into the molecular detoxification mechanisms in silkworms.

CRISPR/Cas9-Mediated Editing of BmEcKL1 Gene Sequence Affected Silk Gland Development of Silkworms (Bombyx mori)

The silkworm (Bombyx mori) has served humankind through silk protein production. However, traditional sericulture and the silk industry have encountered considerable bottlenecks and must rely on major technological breakthroughs to keep up with the current rapid developments. The adoption of gene editing technology has nevertheless brought new hope to traditional sericulture and the silk industry. The long period and low efficiency of traditional genetic breeding methods to obtain high silk-yielding silkworm strains have hindered the development of the sericulture industry; the use of gene editing technology to specifically control the expression of genes related to silk gland development or silk protein synthesis is beneficial for obtaining silkworm strains with excellent traits. In this study, BmEcKL1 was specifically knocked out in the middle (MSGs) and posterior (PSGs) silk glands using CRISPR/Cas9 technology, and ΔBmEcKL1-MSG and ΔBmEcKL1-PSG strains with improved MSGs and PSGs and increased silk production were obtained. This work identifies and proves that BmEcKL1 directly or indirectly participates in silk gland development and silk protein synthesis, providing new perspectives for investigating silk gland development and silk protein synthesis mechanisms in silkworms, which is of great significance for selecting and breeding high silk-yielding silkworm varieties.

Low concentration of indoxacarb interferes with the growth and development of silkworm by damaging the structure of midgut cells

As an important economic insect, Bombyx mori plays an essential role in the development of the agricultural economy. Indoxacarb, a novel sodium channel blocker insecticide, has been widely used for the control of various pests in agriculture and forestry, and its environmental pollution caused by flight control operations has seriously affected the safe production of sericulture in recent years. However, the lethal toxicity and adverse effects of indoxacarb on silkworm remain largely unknown. In this study, the toxicity of indoxacarb on the 5th instar larvae of silkworm was determined, with an LC50 (72 h) of 2.07 mg/L. Short-term exposure (24 h) to a low concentration of indoxacarb (1/2 LC50) showed significantly reduced body weight and survival rate of silkworm larvae. In addition, indoxacarb also led to decreased cocoon weight and cocoon shell weight, but had no significant effects on pupation, adult eclosion, and oviposition. Histopathological and ultrastructural analysis indicated that indoxacarb could severely damage the structure of the midgut epithelial cells, and lead to physiological impairment of the midgut. A total of 3883 differentially expressed genes (DEGs) were identified by midgut transcriptome sequencing and functionally annotated using GO and KEGG. Furthermore, the transcription level and enzyme activity of the detoxification related genes were determined, and our results suggested that esterases (ESTs) might play a major role in metabolism of indoxacarb in the midgut of B. mori. Future studies to examine the detoxification or biotransformation function of candidate genes will greatly enhance our understanding of indoxacarb metabolism in B. mori. The results of this study provide a theoretical basis for elucidating the mechanism of toxic effects of indoxacarb on silkworm by interfering with the normal physiological functions of the midgut.

Decapentaplegic retards lipolysis during metamorphosis in Bombyx mori and Drosophila melanogaster

Insect morphogen decapentaplegic (Dpp) functions as one of the key extracellular ligands of the Bone Morphogenetic Protein (BMP) signaling pathway. Previous studies in insects mainly focused on the roles of Dpp during embryonic development and the formation of adult wings. In this study, we demonstrate a new role for Dpp in retarding lipolysis during metamorphosis in both Bombyx mori and Drosophila melanogaster. CRISPR/Cas9-mediated mutation of Bombyx dpp causes pupal lethality, induces an excessive and premature breakdown of lipids in the fat body, and upregulates the expressions of several lipolytic enzyme genes, including brummer (bmm), lipase 3 (lip3), and hormone-sensitive lipase (hsl), and lipid storage droplet 1 (lsd1), a lipid droplets (LD)-associated protein gene. Further investigation in Drosophila reveals that salivary gland-specific knockdown of the dpp gene and fat body-specific knockdown of Mad involved in Dpp signaling phenocopy the effects of Bombyx dpp mutation on pupal development and lipolysis. Taken together, our data indicate that the Dpp-mediated BMP signaling in the fat body maintains lipid homeostasis by retarding lipolysis, which is necessary for pupa-adult transition during insect metamorphosis.

Amino Acid Substitutions at P1 Position Change the Inhibitory Activity and Specificity of Protease Inhibitors BmSPI38 and BmSPI39 from Bombyx mori

It was found that silkworm serine protease inhibitors BmSPI38 and BmSPI39 were very different from typical TIL-type protease inhibitors in sequence, structure, and activity. BmSPI38 and BmSPI39 with unique structure and activity may be good models for studying the relationship between the structure and function of small-molecule TIL-type protease inhibitors. In this study, site-directed saturation mutagenesis at the P1 position was conducted to investigate the effect of P1 sites on the inhibitory activity and specificity of BmSPI38 and BmSPI39. In-gel activity staining and protease inhibition experiments confirmed that BmSPI38 and BmSPI39 could strongly inhibit elastase activity. Almost all mutant proteins of BmSPI38 and BmSPI39 retained the inhibitory activities against subtilisin and elastase, but the replacement of P1 residues greatly affected their intrinsic inhibitory activities. Overall, the substitution of Gly54 in BmSPI38 and Ala56 in BmSPI39 with Gln, Ser, or Thr was able to significantly enhance their inhibitory activities against subtilisin and elastase. However, replacing P1 residues in BmSPI38 and BmSPI39 with Ile, Trp, Pro, or Val could seriously weaken their inhibitory activity against subtilisin and elastase. The replacement of P1 residues with Arg or Lys not only reduced the intrinsic activities of BmSPI38 and BmSPI39, but also resulted in the acquisition of stronger trypsin inhibitory activities and weaker chymotrypsin inhibitory activities. The activity staining results showed that BmSPI38(G54K), BmSPI39(A56R), and BmSPI39(A56K) had extremely high acid-base and thermal stability. In conclusion, this study not only confirmed that BmSPI38 and BmSPI39 had strong elastase inhibitory activity, but also confirmed that P1 residue replacement could change their activity and inhibitory specificity. This not only provides a new perspective and idea for the exploitation and utilization of BmSPI38 and BmSPI39 in biomedicine and pest control, but also provides a basis or reference for the activity and specificity modification of TIL-type protease inhibitors.

Tandem Multimerization Can Enhance the Structural Homogeneity and Antifungal Activity of the Silkworm Protease Inhibitor BmSPI39

Previous studies have shown that BmSPI39, a serine protease inhibitor of silkworm, can inhibit virulence-related proteases and the conidial germination of insect pathogenic fungi, thereby enhancing the antifungal capacity of Bombyx mori. The recombinant BmSPI39 expressed in Escherichia coli has poor structural homogeneity and is prone to spontaneous multimerization, which greatly limits its development and application. To date, the effect of multimerization on the inhibitory activity and antifungal ability of BmSPI39 remains unknown. It is urgent to explore whether a BmSPI39 tandem multimer with better structural homogeneity, higher activity and a stronger antifungal ability can be obtained by protein engineering. In this study, the expression vectors of BmSPI39 homotype tandem multimers were constructed using the isocaudomer method, and the recombinant proteins of tandem multimers were obtained by prokaryotic expression. The effects of BmSPI39 multimerization on its inhibitory activity and antifungal ability were investigated by protease inhibition and fungal growth inhibition experiments. In-gel activity staining and protease inhibition assays showed that tandem multimerization could not only greatly improve the structural homogeneity of the BmSPI39 protein, but also significantly increase its inhibitory activity against subtilisin and proteinase K. The results of conidial germination assays showed that tandem multimerization could effectively enhance the inhibitory ability of BmSPI39 on the conidial germination of Beauveria bassiana. A fungal growth inhibition assay showed that BmSPI39 tandem multimers had certain inhibitory effects on both Saccharomyces cerevisiae and Candida albicans. The inhibitory ability of BmSPI39 against these the above two fungi could be enhanced by tandem multimerization. In conclusion, this study successfully achieved the soluble expression of tandem multimers of the silkworm protease inhibitor BmSPI39 in E. coli and confirmed that tandem multimerization can improve the structural homogeneity and antifungal ability of BmSPI39. This study will not only help to deepen our understanding of the action mechanism of BmSPI39, but also provide an important theoretical basis and new strategy for cultivating antifungal transgenic silkworms. It will also promote its exogenous production and development and application in the medical field.

Biochemical characterization and overexpression of an α-amylase (BmAmy) in silkworm, Bombyx mori

Silkworm (Bombyx mori) is the only fully domesticated insect. As an economically important insect, nutrition utilization is important for its productivity. Hence, the present study investigated the expression pattern of BmAmy, an α-amylase, in B. mori. BmAmy protein purification and biochemical characterization were performed, and effects of BmAmy overexpression were assessed. Real-time quantitative reverse transcription polymerase chain reaction indicated that BmAmy transcription was positively correlated with the silkworm's food intate. Moreover, enzymatic activity assay results showed that BmAmy had significant α-amylase activity of about 1 mg/min/mg protein. Furthermore, treatment with mulberry amylase inhibitors MnAI1 and MnAI2 resulted to 89.92% and 93.67% inhibition in BmAmy activity, respectively, and the interaction between BmAmy and MnAI was also confirmed by protein docking analysis. A silkworm line that specifically overexpressed BmAmy in the midgut was generated through piggyBac-based transgenic technology, and compared to those of non-transgenic silkworms, the whole cocoon and cocoon shell weights of these transgenic silkworms increased by 10.13% and 18.32%, respectively, in the female group, and by 5.83% and 6.00%, respectively, in the male group. These results suggested that BmAmy may be a suitable target for breeding better silkworm varieties in the future.

Transcriptomic analysis of salivary gland and proteomic analysis of oral secretion in Helicoverpa armigera under cotton plant leaves, gossypol, and tannin stresses

Gossypol and tannin are involved in important chemical defense processes in cotton plants. In this study, we used transcriptomics and proteomics to explore the changes in salivary gland functional genes and oral secretion (OS) proteins after feeding with artificial diet (containing gossypols and tannins) and cotton plant leaves. We found that dietary cotton plant leaves, gossypols and tannins exerted adverse impacts on the genes that regulated the functions of peptidase, GTPase, glycosyl hydrolases in the salivary glands of the Helicoverpa armigera (H. armigera). However, GST, UGT, hydrolases, and lipase genes were up-regulated to participate in the detoxification and digestive of H. armigera. The oral secretory proteins of H. armigera were significantly inhibited under the stress of gossypol and tannin, such as enzyme activity, but some proteins (such as PZC71358.1) were up-regulated and involved in immune and digestive functions. The combined analysis of transcriptomics and metabolomics showed a weak correlation, and the genes and proteins involved were mainly in digestive enzyme activities. Our work clarifies the deleterious physiological impacts of gossypols and tannins on H. armigera and reveals the mechanism by which H. armigera effectively mitigate the phytotoxic effects through detoxification and immune systems.

Genome-wide identification of lipases in silkworm (Bombyx mori) and their spatio-temporal expression in larval midgut

Lipases play crucial roles in food digestion by degrading dietary lipids into free fatty acids and glycerols. The domesticated silkworm (Bombyx mori) has been widely used as an important Lepidopteran model for decades. However, little is known about the lipase gene family in the silkworm, especially their hydrolytic activities as digestive enzymes. In this study, a total of 38 lipase genes were identified in the silkworm genome. Phylogenetic analysis indicated that they were divided into three major groups. Twelve lipases were confirmed to be expressed in the midgut at both transcriptional and translational levels. They were grouped into the same gene cluster, suggesting that they could have similar physiological functions. Quantitative real-time PCR (qRT-PCR) analyses indicated that lipases were mainly expressed in anterior and middle midgut regions, and their expression levels varied greatly along the length of midgut. A majority of lipases were down-regulated in the midgut when larvae stopped feeding. However, a unique lipase gene (Bmlip10583) showed low expression level during feeding stage, but it was significantly up-regulated during the larvae-pupae transition. These results demonstrated that expression of silkworm lipases was spatially and temporally regulated in the midgut during larval development. Taken together, our results provide a fundamental research of the lipase gene family in the silkworm.

Genome-wide survey and characterization of transcription factors in the silk gland of the silkworm, Bombyx mori

Transcription factors (TFs) are key proteins that modulate gene transcription and thereby lead to changes in the gene expression profile and the subsequent alteration of cellular functions. In the silk gland (SG) of silkworm Bombyx mori, an important silk-producing insect, TFs are of vital importance in the regulation of silk protein synthesis in this organ. However, which TFs exist and express in the SG remains largely unknown. Here, we report the large-scale identification of TFs in the SG based on available full-length transcript sequences and the most recent version of silkworm genome data. In total, 348 candidate TFs were identified by strict filtration and were classified into 56 TF families. Chromosomal distribution, motif composition, and phylogenetic relationship analyses revealed the typical characteristics of these TFs. In addition, the expression patterns of 348 TFs in various tissues of B. mori, especially the SG of fourth-molt (4LM) and day-3 and day-4 fifth-instar (5L3D and 5L4D) larvae, were investigated based on public RNA-seq data and gene microarray data, followed by spatiotemporal verification of TF expression levels by quantitative real-time PCR (qRT-PCR). This report describes the first comprehensive analysis of TFs in the B. mori SG. The results can serve as a baseline for further studies of the roles of TFs in the B. mori SG.

Hemolymph Ecdysteroid Titer Affects Maternal mRNAs during Bombyx mori Oogenesis

Simple Summary

Both maternal genes and ecdysteroids play important roles during embryonic development. In this study, we aimed to characterize the dynamic landscape of maternal mRNAs and the relationship between maternal genes and ecdysteroids during silkworm oogenesis. For the first time, we determined the start of the accumulation of maternal mRNAs in the ovary at the wandering stage during the larval period. We detected the developmental expression profiles of each gene in the ovary or ovariole. We finally confirmed the role of 20-hydroxyecdysone in regulating maternal gene expression. Taken together, our findings expand the understanding of insect oogenesis and provide a perspective on the embryonic development of the silkworm.

Abstract

Silkworm larval–pupal metamorphosis and the first half of pupal–adult development occur during oogenesis from previtellogenesis to vitellogenesis and include two peaks of the hemolymph ecdysteroid titer. Moreover, a rise in 20-hydroxyecdysone titer in early pupae can trigger the first major transition from previtellogenesis to vitellogenesis in silkworm oogenesis. In this study, we first investigated the expression patterns of 66 maternal genes in the ovary at the wandering stage. We then examined the developmental expression profiles in six time-series samples of ovaries or ovarioles by reverse transcription–quantitative PCR. We found that the transcripts of 22 maternal genes were regulated by 20-hydroxyecdysone in the isolated abdomens of the pupae following a single injection of 20-hydroxyecdysone. This study is the first to determine the relationship between 20-hydroxyecdysone and maternal genes during silkworm oogenesis. These findings provide a basis for further research into the embryonic development of Bombyx mori.

A Gut-Specific LITAF-Like Gene in Antheraea pernyi (Lepidoptera: Saturniidae) Involved in the Immune Response to Three Pathogens

Antheraea pernyi (Guérin-Méneville 1855) is an important resource for silk, food, and biohealth products; however, exogenous pathogens largely affect the commercial application potential of this species. Since the gut is a key organ for the digestion and absorption of nutrients as well as for immune defense, we used comparative transcriptome analysis to screen for a gut-specific molecular tool for further functional research in A. pernyi. In total, 3,331 differentially expressed genes (DEGs) were identified in the gut compared with all other pooled tissues of A. pernyi, including 1,463 upregulated genes in the gut. Among these, we further focused on a lipopolysaccharide-induced tumor necrosis factor-α factor (LITAF) gene because of its high gut-specific expression and the presence of a highly conserved SIMPLE-like domain, which is related to the immune response to pathogenic infections in many species. The cDNA sequence of ApLITAF was 447-bp long and contained a 243-bp open reading frame encoding an 80-amino acid protein. Immune challenge assays indicated that ApLITAF expression was significantly upregulated in the gut of A. pernyi naturally infected with nucleopolyhedrovirus (NPV) or fed leaves infected with the gram-negative bacterium Escherichia coli (Migula 1895) and the gram-positive bacterium Bacillus subtilis (Ehrenberg 1835). Cell transfection showed that ApLITAF localized to the lysosome. Collectively, these results suggested that ApLITAF played a role in the immune response of A. pernyi and could facilitate the future research and breeding application in this species.

Lineage-specific gene evolution of innate immunity in Bombyx mori to adapt to challenge by pathogens, especially entomopathogenic fungi

Bombyx mori is a model species of Lepidoptera, in which 21 gene families and 220 genes have been identified as involved in immunity. However, only 45 B. mori - Drosophila melanogaster - Anopheles gambiae - Apis mellifera - Tribolium castaneum 1:1:1:1:1 orthologous genes were identified. B. mori has unique immune factors not found in D. melanogaster - A. gambiae - A. mellifera - T. castaneum. Pattern recognition receptors, signal transducers and effector genes for antifungal immune responses in B. mori have evolved through expansion and modification of existing genes. This review summarizes the current knowledge of the antifungal immune responses of B. mori and focuses on the lineage-specific gene evolution used by Lepidoptera to adapt to the challenge by pathogens, especially entomopathogenic fungi.

Molecular basis of the silkworm mutant rel causing red egg color and embryonic death

The coloration and hatchability of insect eggs can affect individual and population survival. However, few genetic loci have been documented to affect both traits, and the genes involved in regulating these two traits are unclear. The silkworm recessive mutant re^l shows both red egg color and embryo mortality. We studied the molecular basis of the re^l phenotype formation. Through genetic analysis, gene screening and sequencing, we found that two closely linked genes, BGIBMGA003497 (Bm-re) and BGIBMGA003697 (BmSema1a), control egg color and embryo mortality, respectively. Six base pairs of the Bm-re gene are deleted in its open reading frame, and BmSema1a is expressed at abnormally low levels in mutant re^l . BmSema1a gene function verification was performed using RNA interference and clustered randomly interspersed palindromic repeats (CRISPR)/CRISPR-associate protein 9. Deficiency of the BmSema1a gene can cause the death of silkworm embryos. This study revealed the molecular basis of silkworm re^l mutant formation and indicated that the Sema1a gene is essential for insect embryo development.

Transcriptomic analysis of the bagworm moth silk gland reveals a number of silk genes conserved within Lepidoptera

Lepidopteran insects produce cocoons with unique properties. The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited. Here, we investigated silk genes in the bagworm moth Eumeta variegata, a species that has recently been found to produce extraordinarily strong and tough silk. Using short-read transcriptomic analysis, we identified a partial sequence of the fibroin heavy chain gene and its product was found to have a C-terminal structure that is conserved within nonsaturniid species. This is in accordance with the presence of fibroin light chain/fibrohexamerin genes and it is suggested that the bagworm moth is producing silk composed of fibroin ternary complex. This indicates that the fibroin structure has been evolutionarily conserved longer than previously thought. Other than fibroins we identified candidates for sericin genes, expressed strongly in the middle region of the silk gland and encoding serine-rich proteins, and other silk genes, that are structurally conserved with other lepidopteran homologues. The bagworm moth is thus considered to be producing conventional lepidopteran type of silk. We further found a number of genes expressed in a specific region of the silk gland and some genes showed conserved expression with Bombyx mori counterparts. This is the first study allowing comprehensive silk gene identification and expression analysis in the lepidopteran Psychidae family and should contribute to the understanding of silk gene evolution as well as to the development of novel types of silk.

Reference Transcriptome Data in Silkworm Bombyx mori

Herein, we performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. The sequences were mapped onto the reference genome assembly and the reference transcriptome data were successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly improved the gene model for other genes. The transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified. We successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research as well as the practical use of these insects.

Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB)

Silkworm Bombyx mori is an economically important insect and a lepidopteran model. Organelle proteome is vital to understanding gene functions; however, it remains to be identified in silkworm. Here, using the engineered ascorbate peroxidase APEX, we constructed transgenic B. mori embryo cells (BmE) expressing APEX-NLS, COX4-APEX, APEX-Rev, and APEX-KDEL in nucleus, mitochondrial matrix (MM), cytosol, and endoplasmic reticulum (ER), and isolated the biotin-labeled proteins using streptavidin-affinity purification, respectively. The isolated proteins were determined using LC-MS/MS and annotated by searching B. mori genomes downloaded from GenBank, SilkBase, SilkDB 2.0, and SilkDB 3.0, resulting in 842, 495, 311, and 445 organelle proteins identified, respectively. We mapped the 296 MM proteins annotated in the GenBank data to mitochondrial protein databases of the fly, human, and mouse, and found that 140 (47%) proteins are homologous to 80 fly proteins, and 65 (22%) proteins match to 31 and 29 human and mouse proteins, respectively. Protein orthology was predicted in multiple insects using OrthoMCL, producing 460 families containing 839 proteins we identified. Out of 460 families, 363 were highly conserved and found in all insects, leaving only three proteins without orthology in other insects, indicating that the identified proteins are highly conserved and probably play important roles in insects. A gene ontology enrichment analysis by clusterProfiler revealed that the nucleus proteins significantly enriched in cellular component terms of nucleus and nucleolus, the MM proteins markedly enriched in molecular function terms of nucleotide binding, and the cytosol proteins mainly enriched in biological process terms of small molecule metabolism. To facilitate the usage and analysis of our data, we developed an open-access database, Silkworm Organelle Proteome Database (SilkOrganPDB), which provides multiple modules for searching, browsing, downloading, and analyzing these proteins, including BLAST, HMMER, Organelle Proteins, Protein Locations, Sequences, Gene Ontology, Homologs, and Phylogeny. In summary, our work revealed the protein composition of silkworm BmE organelles and provided a database resource helpful for understanding the functions and evolution of these proteins.

Target antifungal peptides of immune signalling pathways in silkworm, Bombyx mori, against Beauveria bassiana

Antifungal innate immunity is an important defence used by insects against entomogenous fungi. However, the downstream target antifungal peptides of different immune signalling pathways are unknown. We found that the Toll, Janus kinase/signal transducer and activator of transcription (Jak/STAT) and Immunodeficiency (IMD) signalling pathways in the silkworm, Bombyx mori, can be activated by Beauveria bassiana. Inhibition of the Toll, IMD and Jak/STAT signalling pathways reduced the antifungal activities of silkworm haemolymph. We verified the target antifungal peptides of different immune signalling pathways. The expression patterns of five anti-fungal peptide genes in silkworm larvae and BmN cells were detected after blocking or over-expressing the immune signalling pathways. The Toll signalling pathways mediated the expression of Bmcecropin A, Bmattacin 1 and Bmgloverin 2; IMD signalling pathways mediated Bmenbocin 1, Bmgloverin 2 and Bmattacin 1; Jak/STAT signalling pathways mediated Bmstorage protein 30K-19G1 (Bmsp 1), Bmattacin 1 and Bmcecropin A. These data indicated that anti-microbial peptide genes in B. mori evolved through expansion and selection of existing genes to adapt to the challenge of invasive microorganisms such as fungi. This information provides insight into the antifungal immune responses in B. mori and aids understanding of insect immune regulation mechanisms.

Molecular cloning, expression, and characterization of BmSOD3 in silkworm (Bombyx mori)

Superoxide dismutases (SODs) play an essential role in eliminating excess reactive oxygen species and maintaining the redox balance of the immune system. To study the function of BmSOD3 in silkworm, 543-bp full-length complementary DNA-encoding BmSOD3 was cloned from silkworm. The BmSOD3 amino acids were compared to their homologs, and several highly conserved regions were analyzed. We also carried out phylogenetic analyses of the SOD gene. Our results showed that the BmSOD3 gene belonged with the ecCu/Zn SOD gene. The BmSOD3 gene was transformed into the pET28a vector for functional expression in Escherichia coli. The sodium salt-polyacrylamide gel electrophoresis results showed that the molecular weight of recombinant BmSOD3 was about 22 kDa. The recombinant protein BmSOD3 was purified to detect its properties. After purification analyses, the enzyme activity showed Cu/Zn SOD activity, and the specific activity of the purified enzyme was 0.51 U/mg. The BmSOD3 transcripts showed tissue-specific expression in the midgut and malpighian tubule. The immune microarray data for BmSOD3 showed an expression signal that had a strong response to the induction of four pathogens (Bacillus bombyseptieus, Beauveria bassiana, E. coli, and nuclear polyhedrosis virus), particularly after infection for 24 h, which indicates that the BmSOD3 gene plays a key role in response to bacterial, fungal, and viral invasion. The fusion protein also showed antibacterial activity against E. coli in vitro. Thus, the fusion protein BmSOD3 exhibits antibacterial activity and may be used in production to combat diseases caused by bacteria in silkworm.

Genome-wide identification and analysis of the thiolase family in insects

Thiolases are important enzymes involved in lipid metabolism in both prokaryotes and eukaryotes, and are essential for a range of metabolic pathways, while, little is known for this important family in insects. To shed light on the evolutionary models and functional diversities of the thiolase family, 137 thiolase genes were identified in 20 representative insect genomes. They were mainly classified into five classes, namely cytosolic thiolase (CT-thiolase), T1-thiolase, T2-thiolase, trifunctional enzyme thiolase (TFE-thiolase), and sterol carrier protein 2 thiolase (SCP2-thiolase). The intron number and exon/intron structures of the thiolase genes reserve large diversification. Subcellular localization prediction indicated that all the thiolase proteins were mitochondrial, cytosolic, or peroxisomal enzymes. Four highly conserved sequence fingerprints were found in the insect thiolase proteins, including CxS-, NEAF-, GHP-, and CxGGGxG-motifs. Homology modeling indicated that insect thiolases share similar 3D structures with mammals, fishes, and microorganisms. In Bombyx mori, microarray data and reverse transcription-polymerase chain reaction (RT-PCR) analysis suggested that some thiolases might be involved in steroid metabolism, juvenile hormone (JH), and sex pheromone biosynthesis pathways. In general, sequence and structural characteristics were relatively conserved among insects, bacteria and vertebrates, while different classes of thiolases might have differentiation in specific functions and physiological processes. These results will provide an important foundation for future functional validation of insect thiolases.

Ingestion and effects of polystyrene nanoparticles in the silkworm Bombyx mori

Information on the occurrence and effects of nanoplastics in ecosystems worldwide currently represent one of the main challenges from the ecotoxicological point of view. This is particularly true for terrestrial environments, in which nanoplastics are released directly by human activities or derive from the fragmentation of larger plastic items incorrectly disposed. Since insects can represent a target for these emerging contaminants in land-based community, the aim of this study was the evaluation of ingestion of 0.5 μm polystyrene nanoplastics and their effects in silkworm (Bombyx mori) larvae, a useful and well-studied insect model. The ingestion of nanoplastics, the possible infiltration in the tissues and organ accumulation were checked by confocal microscopy, while we evaluated the effects due to the administered nanoplastics through a multi-tier approach based on insect development and behaviour assessment, as endpoints at organism level, and the measurements of some biochemical responses associated with the imbalance of the redox status (superoxide dismutase, catalase, glutathione s-transferase, reactive oxygen species evaluation, lipid peroxidation) to investigate the cellular and molecular effects. We observed the presence of microplastics in the intestinal lumen, but also inside the larvae, specifically into the midgut epithelium, the Malpighian tubules and in the haemocytes. The behavioural observations revealed a significant (p < 0.05) increase of erratic movements and chemotaxis defects, potentially reflecting negative indirect effects on B. mori survival and fitness, while neither effect on insect development nor redox status imbalance were measured, with the exception of the significant (p < 0.05) inhibition of superoxide dismutase activity.

Responses of detoxification enzymes in the midgut of Bombyx mori after exposure to low-dose of acetamiprid

Bombyx mori is an important economic insect. However, the environmental pollution caused by the widespread use of neonicotinoid insecticides has significantly affected the safe production of sericulture. In this paper, we determined the LC₅₀ of acetamiprid, a kind of neonicotinoid insecticides, to 5th instar silkworm larvae, examined its residues in hemolymph and midgut of silkworm after continuous exposure to low-dose of acetamiprid, and investigated the transcription level of detoxifying-related genes and the activity of detoxifying enzymes. The results showed that acetamiprid was highly toxic (24-h LC₅₀, 1.50 mg/L) to silkworm larvae. After continuous exposure to low-dose of acetamiprid (0.15 mg/L), the acetamiprid residue concentrations in hemolymph and midgut were 0.90 and 0.58 μg/mg, respectively, at 48 h, but all decreased at 96 h. At 24 h of acetamiprid exposure, the transcription levels of CYP4M5 and CYP6AB4 and the P450 enzyme activity were significantly enhanced. However, the transcription levels of CarE and CarE-11 and the activity of CarE enzymes were both inhibited by acetamiprid exposure. After 24 h-72 h of acetamiprid exposure, the transcription levels of GSTe3 and GSTd1 were significantly up-regulated, and the GST enzyme activity was also significantly elevated from 48 h to 96 h. Furthermore, the expression levels of FoxO, CncC and Keap1, the key upstream genes of detoxification enzymes, showed a similar trend as the GST genes. These results indicated that acetamiprid was reduced in midgut and the expression of GSTs was upregulated may via FoxO/CncC/Keap1 signaling pathway, which plays a key role in detoxification responses.

A transcriptome atlas of silkworm silk glands revealed by PacBio single-molecule long-read sequencing

The silk gland of the silkworm Bombyx mori is a specialized organ where silk proteins are efficiently synthesized under precise regulation that largely determines the properties of silk fibers. To understand the genes involved in the regulation of silk protein synthesis, considerable research has focused on the transcripts expressed in silk glands; however, the complete transcriptome profile of this organ has yet to be elucidated. Here, we report a full-length silk gland transcriptome obtained by PacBio single-molecule long-read sequencing technology. In total, 11,697 non-redundant transcripts were identified in mixed samples of silk glands dissected from larvae at five developmental stages. When compared with the published reference, the full-length transcripts optimized the structures of 3002 known genes, and a total of 9061 novel transcripts with an average length of 2171 bp were detected. Among these, 1403 (15.5%) novel transcripts were computationally revealed to be lncRNAs, 8135 (89.8%) novel transcripts were annotated to different protein and nucleotide databases, and 5655 (62.4%) novel transcripts were predicted to have complete ORFs. Furthermore, we found 1867 alternative splicing events, 2529 alternative polyadenylation events, 784 fusion events and 6596 SSRs. This study provides a comprehensive set of reference transcripts and greatly revises and expands the available silkworm transcript data. In addition, these data will be very useful for studying the regulatory mechanisms of silk protein synthesis.

Excess melanin precursors rescue defective cuticular traits in stony mutant silkworms probably by upregulating four genes encoding RR1-type larval cuticular proteins

Melanin and cuticular proteins are vital cuticle components in insects. Cuticular defects caused by mutations in cuticular protein-encoding genes can obstruct melanin deposition. The effects of changes in melanin on the expression of cuticular protein-encoding genes, the cuticular and morphological traits, and the origins of these effects are unknown. We found that the cuticular physical characteristics and the expression patterns of larval cuticular protein-encoding genes markedly differed between the melanic and non-melanic integument regions. By using four p multiple-allele color pattern mutants with increasing degrees of melanism (+^p, p^M, p^S, and p^B), we found that the degree of melanism and the expression of four RR1-type larval cuticular protein-encoding genes (BmCPR2, BmLcp18, BmLcp22, and BmLcp30) were positively correlated. By modulating the content of melanin precursors and the expression of cuticular protein-encoding genes in cells in tissues and in vivo, we showed that this positive correlation was due to the induction of melanin precursors. More importantly, the melanism trait introduced into the BmCPR2 deletion strain Dazao-stony induced up-regulation of three other similar chitin-binding characteristic larval cuticular protein-encoding genes, thus rescuing the cuticular, morphological and adaptability defects of the Dazao-stony strain. This rescue ability increased with increasing melanism levels. This is the first study reporting the induction of cuticular protein-encoding genes by melanin and the biological importance of this induction in affecting the physiological characteristics of the cuticle.

Transcriptome analysis reveals gene expression changes of the fat body of silkworm (Bombyx mori L.) in response to selenium treatment

A comparative transcriptome analysis was conducted to investigate the gene expression changes in the fat body of silkworm after treatment with different concentrations (50 μM and 200 μM) of selenium (Se). 912 differential expression genes (DEGs) (371 up-regulated and 541 down-regulated) and 1420 DEGs (1078 up-regulated and 342 down-regulated) were identified in silkworm fat body treated with 50 μM and 200 μM of Se, respectively. In case of 50 μM group, DEGs were mainly enriched in the peroxisome pathway and fatty acid metabolism pathway, and later were associated with antioxidant defense and nutrition regulation. After 200 μM Se-treatment, DEGs were mainly located in the glycerolipid metabolism and arachidonic acid metabolism pathways, which further encoded detoxification related genes. Furthermore, 32 candidate DEGs from these pathways had been selected to confirm the RNA-seq data. Among these DEGs, 14 genes were up-regulated in the 50 μM Se-treated group (only three genes in the 200 μM Se-treated group) which were involved in lipid metabolism and antioxidant defense, and 13 up-regulated genes (only two genes were up-regulated in the 50 μM Se-treated group) were involved in detoxification of the 200 μM Se-treated group. These changes showed that lower concentration of Se could regulate the nutrition and promote antioxidation pathways; whereas, high levels of Se promoted the detoxification of silkworm. These findings can be helpful to understand the possible mechanisms of Se action and detoxification in silkworm and other insects.

iTRAQ-Based Quantitative Proteomic Analysis of Digestive Juice across the First 48 Hours of the Fifth Instar in Silkworm Larvae

The silkworm is an oligophagous insect for which mulberry leaves are the sole diet. The nutrients needed for vital activities of the egg, pupal, and adult stages, and the proteins formed in the cocoon, are all derived from the larval stages. The silkworm feeds and grows quickly during the larval stages. In particular, the amount of leaf ingested and digested quickly increases from the ecdysis to the gluttonous stage in the fifth instar period. In this study, we used the iTRAQ proteomic technique to identify and analyze silkworm larval digestive juice proteins during this period. A total of 227 proteins were successfully identified. These were primarily serine protease activity, esterase activity, binding, and serine protease inhibitors, which were mainly involved in the digestion and overcoming the detrimental effects of mulberry leaves. Moreover, 30 genes of the identified proteins were expressed specifically in the midgut. Temporal proteomic analysis of digestive juice revealed developmental dynamic features related to molecular mechanisms of the principal functions of digesting, resisting pathogens, and overruling the inhibitory effects of mulberry leaves protease inhibitors (PIs) with a dynamic strategy, although overruling the inhibitory effects has not yet been confirmed by previous study. These findings will help address the potential functions of digestive juice in silkworm larvae.

BmBlimp-1 gene encoding a C2H2 zinc finger protein is required for wing development in the silkworm Bombyx mori

Cys2-His2 zinc finger (C2H2-ZF) proteins represent the most common class of transcription factors. These factors have great potential for the management of developmental progression by regulating the specific spatiotemporal expression of genes. In this study, we cloned one C2H2-ZF protein gene of Bombyx mori, BGIBMGA000319, that is orthologous to B-lymphocyte-induced maturation protein-1 (Blimp-1); we thus named it as Bombyx mori Blimp-1 (BmBlimp-1). In the silkworm, the BmBlimp-1 gene is specifically upregulated during day 2 of the pupal to adult stage and is highly expressed in wing discs on day 3 of the pupa. Knockdown of its expression level in the pupal stage results in a crumpled-winged silkworm moth. Using the predicted DNA-binding sequences of BmBlimp-1 to search the silkworm genome to screen target genes of BmBlimp-1, 7049 genes were identified to have at least one binding site of BmBlimp-1 on their 1 kb upstream and downstream genome regions. Comparisons of those genes with a reported pupal wing disc transcriptome data resulted in 4065 overlapping genes being retrieved. GO enrichment analysis of the overlapping genes showed that most of the genes were enriched in the binding term. Combining functional annotation and real-time quantitative PCR, 15 genes were identified as the candidate target genes of BmBlimp-1, including several wing cuticular protein genes, chitin synthase A, and wing disc development genes, such as Wnt1, cubitus interruptus (ci) and engrailed (en). Moreover, the amino acid sequence of the zinc finger motif of Blimp-1 gene was highly conserved among the 15 insect species. We propose that BmBlimp-1 is an important regulatory factor in silkworm wing development.

Expression Analysis of mRNA Decay of Maternal Genes during Bombyx mori Maternal-to-Zygotic Transition

Maternal genes play an important role in the early embryonic development of the silkworm. Early embryonic development without new transcription depends on maternal components stored in the egg during oocyte maturation. The maternal-to-zygotic transition (MZT) is a tightly regulated process that includes maternal mRNAs elimination and zygotic transcription initiation. This process has been extensively studied within model species. Each model organism has a unique pattern of maternal transcriptional clearance classes in MZT. In this study, we identified 66 maternal genes through bioinformatics analysis and expression analysis in the eggs of silkworm virgin moths (Bombyx mori). All 66 maternal genes were expressed in vitellogenesis in day eight female pupae. During MZT, the degradation of maternal gene mRNAs could be divided into three clusters. We found that eight maternal genes of cluster 1 remained stable from 0 to 3.0 h, 17 maternal genes of cluster 2 were significantly decayed from 0.5 to 1.0 h and 41 maternal genes of cluster 3 were significantly decayed after 1.5 h. Therefore, the initial time-point of degradation of cluster 2 was earlier than that of cluster 3. The maternal gene mRNAs decay of clusters 2 and 3 is first initiated by maternal degradation activity. Our study expands upon the identification of silkworm maternal genes and provides a perspective for further research of the embryo development in Bombyx mori.

Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil's geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.

Comparative analysis of integument transcriptomes identifies genes that participate in marking pattern formation in three allelic mutants of silkworm, Bombyx mori

The diversity markings and pigment patterns in insects are outcomes of adaptive evolution. The elucidation of the molecular mechanism underlying variations in pigment patterns may improve our understanding of the origin and evolution of these spectacular diverse phenotypes. Melanin, ommochrome, and pteridine are the three main types of insect pigments, and the genes that directly participate in pigment biosynthesis have been extensively studied. However, available information on gene interactions and the whole pigment regulatory network is limited. In this study, we performed integument transcriptome sequencing to analyze three larval marking allelic mutants, namely, multi lunar (L), L^C, and L^Ca, which have similar twin-spot markings on the dorsal side of multiple segments. Further analysis identified 336 differentially expressed genes (DEGs) between L and Dazao (wild type which exhibits normal markings), 68 DEGs between L^C/+ and +^LC/+^LC, and 188 DEGs between L^Ca/+ and +^LCa/+^LCa. Gene Ontology (GO) analysis indicated a significant DEG enrichment of the functional terms catalytic activity, binding, metabolic process, and cellular process. Furthermore, three mutants share six common enriched KEGG pathways. We finally identified eight common DEGs among three pairwise comparisons, including Krueppel-like factor, TATA-binding protein, protein patched, UDP-glycosyltransferase, an unknown secreted protein, and three cuticular proteins. Microarray-based gene expression analysis revealed that the eight genes are upregulated during molting, which coincides with marking formation, and are significantly differentially expressed between marking and non-marking regions. The results suggest that the eight common genes are involved in the construction of the multiple twin-spot marking patterns in the three mutants.

Comparative proteomic analysis of sex-biased proteins in ovary and testis at different stages of Spodoptera litura

Sex-biased protein is thought to be able to drive the phenotypic differences in males and females in insects. In this study, 1385 and 1727 proteins were identified as differentially accumulated proteins (DAPs) by comparing the protein abundances at pupae stage with those at adult stage in ovary and testis of S.litura, respectively. And among which, 548 DAPs were showed to be expressed in both ovary and testis, and 837 and 1179 proteins were considered as ovary-specific and testis-specific DAPs, respectively. To further identify DAPs related to gonad development and sex dimorphism, a total of 320 DAPs were selected and defined as "proteins of specific interest" based on several selecting criteria. Sex dimorphism is a complex and dynamic developmental progress, and these identified DAPs were suggested to be involved in multiple functions such as organonitrogen compound catabolic process, glycosylation, proteasome, N-Glycan biosynthesis and other reproduction-related processes. Overall, our results highlighted these sexual-biased, gonad development related and sexual dimorphism related DAPs, and their abundance variations along with development were also examined, which could provide important information for their functional analysis in reproduction and potential biomarkers for developing useful strategies against S. litura and other orthologous pests. BIOLOGICAL SIGNIFICANCE: Sex dimorphism entails the differentiation of two sexual functions, resulting in sexually phenotypic differences and leading to the development of female and male morphologies and behaviors. However, sex dimorphism related proteins remain to be identified in many non-model insects. In this study, iTRAQ-based proteomic analysis was applied to examine the variations of protein abundances at pupae stage and adult stage in ovary and testis of S.litura, respectively. Reproduction and sex dimorphism related proteins were further identified as "proteins of specific interest". These identified candidate proteins provided valuable information for their further functional analysis in reproduction and could serve as potential biomarkers for developing useful strategies against S. litura and other orthologous pests.

Construction of a simple evaluation system for the intestinal absorption of an orally administered medicine using Bombyx mori larvae

Human intestinal absorption is estimated using a human colon carcinoma cell line (Caco-2) cells from human colorectal adenocarcinoma, intestinal perfusion, or a mammalian model. These current evaluation systems are limited in their ability to estimate human intestinal absorption. In addition, in vivo evaluation systems using laboratory animals such as mice and rats entail animal ethics problems, and it is difficult to screen compounds on a large scale at the drug discovery stage. Thus, we propose the use of Bombyx mori larvae for evaluation of intestinal absorption of compounds as an alternative system in this study. First, to compare the characteristics among Caco-2 cells, human intestine, and B. mori larval midgut, we analyzed their RNA-seq data, and we found 26 drug transporters common to humans and B. mori. Next, we quantitatively developed an oral administration technique in B. mori and established a method using silkworm B. mori larvae that can easily estimate the intestinal permeability of compounds. Consequently, we could determine the dose and technique for oral administration in B. mori larvae. We also developed a B. mori model to evaluate the intestinal permeability of orally administered. Our constructed evaluation system will be useful for evaluating intestinal permeability in medical drug development.

Specific genes related to nucleopolyhedrovirus in Bombyx mori susceptible and near-isogenic resistant strains through comparative transcriptome analysis

Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the primary pathogens that causes severe economic losses to sericulture. Comparative transcriptomics analysis has been widely applied to explore the antiviral mechanism in resistant strains. Here, to identify genes involved in BmNPV infection, we identified differentially expressed genes (DEGs) and performed weighted gene co-expression network analysis (WGCNA) between two Bombyx mori strains: strain 871 (susceptible to BmNPV infection) and the near-isogenic strain 871C (resistant to BmNPV). Our results showed that 400 genes were associated with resistance in strain 871C, and 76 genes were related to susceptibility in strain 871. In addition, the correlation analysis of DEGs and WGCNA showed that 40 genes related to resistance were highly expressed in the resistant strain. Among them, gene BGIBMGA004291 was the most noticeable. We further identified the effect of gene BGIBMGA004291, which encoded a multiprotein bridge factor 2 (MBF2) family member (MBF2-10), on viral infection in cells. Our data suggested that MBF2-10 inhibited viral infection. Taken together, this study showed specific module trait correlations related to viral infection in strains 871 and 871C, and we identified a resistance-related gene. These findings suggested promising candidate genes with antiviral activity, aiding in the analysis of the antiviral molecular mechanisms in resistant strains.

Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori

Cys2-His2 zinc finger (C2H2-ZF) proteins comprise the largest class of putative eukaryotic transcription factors. The zinc finger motif array is highly divergent, indicating that most proteins will have distinctive binding sites and perform different functions. However, the binding sites and functions of the majority of C2H2-ZF proteins remain unknown. In this study, we identified 327 C2H2-ZF protein genes in the silkworm, 290 in the monarch butterfly, 243 in the fruit fly, 107 in elegans, 673 in mouse, and 1,082 in human. The C2H2-ZF protein genes of the silkworm were classified into three main grouping clades according to a phylogenetic classification, and 312 of these genes could be mapped onto 27 chromosomes. Most silkworm C2H2-ZF protein genes exhibited specific expression in larval tissues. Furthermore, several C2H2-ZF protein genes had sex-specific expression during metamorphosis. In addition, we found that some C2H2-ZF protein genes are involved in metamorphosis and female reproduction by using expression clustering and gene annotation analysis. Among them, five genes were selected, BGIBMGA002091 (CTCF), BGIBMGA006492 (fru), BGIBMGA006230 (wor), BGIBMGA004640 (lola), and BIGBMGA004569, for quantitative real-time PCR analysis from larvae to adult ovaries. The results showed that the five genes had different expression patterns in ovaries, among which BGIBMGA002091 (CTCF) gene expression level was the highest, and its expression level increased rapidly in late pupae and adult stages. These findings provide a basis for further investigation of the functions of C2H2-ZF protein genes in the silkworm, and the results offer clues for further research into the development of metamorphosis and female reproduction in the silkworm.

Genome-wide identification of chitin-binding proteins and characterization of BmCBP1 in the silkworm, Bombyx mori

The insect cuticle plays important roles in numerous physiological functions to protect the body from invasion of pathogens, physical injury and dehydration. In this report, we conducted a comprehensive genome-wide search for genes encoding proteins with peritrophin A-type (ChtBD2) chitin-binding domain (CBD) in the silkworm, Bombyx mori. One of these genes, which encodes the cuticle protein BmCBP1, was additionally cloned, and its expression and location during the process of development and molting in B. mori were investigated. In total, 46 protein-coding genes were identified in the silkworm genome, including those encoding 15 cuticle proteins analogous to peritrophins with one CBD (CPAP1s), nine cuticle proteins analogous to peritrophins with three CBD (CPAP3s), 15 peritrophic membrane proteins (PMPs), four chitinases, and three chitin deacetylases, which contained at least one ChtBD2 domain. Microarray analysis indicated that CPAP-encoding genes were widely expressed in various tissues, whereas PMP genes were highly expressed in the midgut. Quantitative polymerase chain reaction and western blotting showed that the cuticle protein BmCBP1 was highly expressed in the epidermis and head, particularly during molting and metamorphosis. An immunofluorescence study revealed that chitin co-localized with BmCBP1 at the epidermal surface during molting. Additionally, BmCBP1 was notably up-regulated by 20-hydroxyecdysone treatment. These results provide a genome-level view of the chitin-binding protein in silkworm and suggest that BmCBP1 participates in the formation of the new cuticle during molting.

Systemic disruption of the homeostasis of transfer RNA isopentenyltransferase causes growth and development abnormalities in Bombyx mori

Isopentenylation at A37 (i⁶ A37) of some transfer RNAs (tRNAs) plays a vital role in regulating the efficiency and fidelity of protein synthesis. However, whether insects, which are well known for their highly efficient protein synthesis machinery, employ this regulatory mechanism remains uninvestigated. In the current study, a candidate tRNA isopentenyltransferase (IPT) gene with three alternative splicing isoforms (BmIPT1-BmIPT3) was identified in Bombyx mori (silkworm). Only BmIPT1 could complement a yeast mutant lacking tRNA IPT. Phylogenetic analysis showed that silkworm tRNA IPT is conserved in the Lepidoptera. BmIPT was expressed in all B. mori tissues and organs that were investigated, but was expressed at a significantly higher level in silk glands of the fourth instar compared to the first day of the fifth instar. Interestingly, BmIPT was expressed at a significantly higher level in the domesticated silkworm, B. mori, than in wild Bombyx mandarina in multiple tissues and organs. Knock-down of BmIPT by RNA interference caused severe abnormalities in silk spinning and metamorphosis. Constitutive overexpression of BmIPT1 using a cytoplasmic actin 4 promoter in B. mori raised its messenger RNA level more than sixfold compared with nontransgenic insects and led to significant decreases in the body weight and cocoon shell ratio. Together, these results confirm the first functional tRNA IPT in insects and show that a suitable expression level of tRNA IPT is vital for silk spinning, normal growth, and metamorphosis. Thus, i⁶ A modification at position A37 in tRNA probably plays an important role in B. mori protein synthesis.

Genome-wide identification and characterization of myosin genes in the silkworm, Bombyx mori

Myosins are a large family of actin filament-based motor proteins with a broad range of functions such as intracellular membrane trafficking, endocytosis, exocytosis, organellar transport, growth cone motility, cytokinesis, and cell locomotion. They are found in many organisms from fungi to humans. The myosin gene family in Bombyx mori is poorly studied, even though the molecular functions of these genes in vertebrates and insects, such as Drosophila, are well known. We identified 16 myosin genes from B. mori and identified the myosin genes in 12 vertebrates, eight insects, three nematodes, and seven protozoa. The number of myosin genes in vertebrates is double the number in invertebrates. The number of myosin isoforms in classes I and II is larger in vertebrates compared to invertebrates. B. mori myosin genes can be classified into 11 classes. Compared to B. mori, some myosin classes are not present in other insects. Classes I, II, XVIII, and XXI appear to be important for insect survival because they are conserved among nine insects. The relatively large sizes of B. mori myosin genes are due to their longer introns. Reverse transcription PCR (RT-PCR) and quantitative real-time PCR (qRT-PCR) analysis demonstrated that many B. mori myosin genes have tissue-specific expression and exhibit temporal-specific activity during metamorphosis. These data provide insights into evolutionary and functional aspects of B. mori myosin genes that could be useful for the study of homologous myosins in other Lepidoptera species.

The fungal-resistance factors BmSPI38 and BmSPI39 predominantly exist as tetramers, not monomers, in Bombyx mori

Previous studies have indicated that trypsin inhibitor-like cysteine-rich domain (TIL)-type protease inhibitors, BmSPI38 and BmSPI39, suppress conidial germination and integument penetration of entomopathogenic fungi by inhibiting their cuticle-degrading proteases and might functions as fungal-resistance factors in the silkworm. To date, the physiological forms and functional significance of multimerization of BmSPI38 and BmSPI39 remain unknown. In this study, we investigated the physiological forms of BmSPI38 and BmSPI39 in Bombyx mori silkworms using multiple complementary methods, including activity staining, reducing and nonreducing sodium dodecyl sulfate polyacrylamide gel electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, western blotting and immunofluorescence. We found that recombinant BmSPI38 and BmSPI39 tend to form homologous multimers, and their dimers, trimers and tetramers possessed intense inhibitory activity against subtilisin A from Bacillus licheniformis. In contrast, their monomers showed no detectable inhibitory activity. Both BmSPI38 and BmSPI39 also exist mainly as stable tetramers in silkworm tissues, and they also predominantly function as a tetramer in these tissues. This study is the first to demonstrate this preferred quaternary form of a TIL-type protease inhibitor and will likely help to elucidate the mechanisms of BmSPI38 and BmSPI39 in the innate immune response of the silkworm.

Applying microarray-based technique to study and analyze silkworm (Bombyx mori) transcriptomic response to long-term high iron diet

To investigate the biological processes affected by long-term iron supplementation, newly hatched silkworms were exposed to high iron mulberry diet (10 and 100 ppm) and its effect on silkworm transcriptom was determined. The results showed that the silkworm was responsive to iron by increasing iron concentration and ferritin levels in the hemolymph and by regulating the expression of many other genes. A total of 523 and 326 differentially expressed genes were identified in 10 and 100 ppm Fe group compared to the control, respectively. Of these genes, 249 were shared between in both the 10 ppm and 100 ppm Fe group, including 152 up-regulated and 97 down-regulated genes. These shared genes included 19 known Fe regulated, 24 immune-related, 12 serine proteases and serine proteases homologs, 41 cuticular and cuticle genes. Ten genes (carboxypeptidases A, serine protease homologs 85, fibrohexamerin/P25, transferrin, sex-specific storage-protein 2, fungal protease inhibitor F, insect intestinal mucin, peptidoglycan recognition protein B, cuticle protein CPH45, unknown gene) were involved in the regulation of iron overload responses.

Evidence of peripheral olfactory impairment in the domestic silkworms: insight from the comparative transcriptome and population genetics

BACKGROUND

The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori has changed greatly since domestication from B. mandarina, and its olfactory response to environmental odorants clearly decreased. However, the mechanisms that result in the olfactory impairment are largely unknown.

RESULTS

The antennal transcriptomes were compared between the domestic and wild silkworms. Comparison of the same sex between the domestic and wild silkworms revealed 1410 and 1173 differentially expressed genes (DEGs) in males and females, respectively. To understand the olfactory impairment, we mainly focused on the olfactory-related genes. In total, 30 olfactory genes and 19 odorant-degrading enzymes (ODEs) showed differential expression in the two comparisons, in which 19 and 14 were down-regulated in the domestic silkworm, respectively. Based on population genomic data, the down-regulated odorant receptors (ORs) showed a higher ratio of unique non-synonymous polymorphisms to synonymous polymorphisms (N/S ratio) in the domestic populations than that in the wild silkworms. Furthermore, one deleterious mutation was found in OR30 of the domestic population, which was located in transmembrane helix 6 (TM6).

CONCLUSIONS

Our results suggested that down-regulation of the olfactory-related genes and relaxed selection might be the major reasons for olfactory impairment of the domestic silkworm reared completely indoor environment. Reversely, wild silkworm may increase expression and remove deleterious polymorphisms of olfactory-related genes to retain sensitive olfaction.

A functional polypeptide N-acetylgalactosaminyltransferase (PGANT) initiates O-glycosylation in cultured silkworm BmN4 cells

Mucin-type O-glycosylation is initiated by UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts or PGANTs), attaching GalNAc to serine or threonine residue of a protein substrate. In the insect model from Lepidoptera, silkworm (Bombyx mori), however, O-glycosylation pathway is totally unexplored and remains largely unknown. In this study, as the first report regarding protein O-glycosylation analysis in silkworms, we verified the O-glycan profile that a common core 1 Gal (β1-3) GalNAc disaccharide branch without terminally sialylated structure is mainly formed for a baculovirus-produced human proteoglycan 4 (PRG4) protein. Intriguingly, functional screenings in cultured silkworm BmN4 cells for nine Bmpgants reveal that Bmpgant2 is the solo functional BmPGANT for PRG4, implying that Bmpgants may have unique cell/tissue or protein substrate preferences. Furthermore, a recombinant BmPGANT2 protein was successfully purified from silkworm-BEVS and exhibited a high ability to transfer GalNAc for both peptide and protein substrates. Taken together, the present results clarified the functional BmPGANT2 in cultured silkworm cells, providing crucial fundamental insights for future studies dissecting the detailed silkworm O-glycosylation pathways and productions of glycoproteins with O-glycans.

Selection of reference genes for tissue/organ samples on day 3 fifth-instar larvae in silkworm, Bombyx mori

The silkworm, Bombyx mori, is one of the world's most economically important insect. Surveying variations in gene expression among multiple tissue/organ samples will provide clues for gene function assignments and will be helpful for identifying genes related to economic traits or specific cellular processes. To ensure their accuracy, commonly used gene expression quantification methods require a set of stable reference genes for data normalization. In this study, 24 candidate reference genes were assessed in 10 tissue/organ samples of day 3 fifth-instar B. mori larvae using geNorm and NormFinder. The results revealed that, using the combination of the expression of BGIBMGA003186 and BGIBMGA008209 was the optimum choice for normalizing the expression data of the B. mori tissue/organ samples. The most stable gene, BGIBMGA003186, is recommended if just one reference gene is used. Moreover, the commonly used reference gene encoding cytoplasmic actin was the least appropriate reference gene of the samples investigated. The reliability of the selected reference genes was further confirmed by evaluating the expression profiles of two cathepsin genes. Our results may be useful for future studies involving the quantification of relative gene expression levels of different tissue/organ samples in B. mori.

Comparative transcriptome analysis of silkworm, Bombyx mori colleterial gland suggests their functional role in mucous secretion

Colleterial glands (CG) present in the body of adult female of Bombyx mori, which can help adhere eggs on the surface of the host plants. Although this organ has been known for centuries, only morphology and its secretions have been studied. Their gene expression profiles and physiological roles remain largely unknown. Aided by high-throughput next generation sequencing (NGS), we reported the comparative transcriptome analysis of CG isolated from the H9 and the P50 strains of Bombyx mori. A total of 19,896,957 and 20,446,366 clean reads were obtained from CG of H9 and the P50 strains, respectively; then differential expression analysis was performed, and 1,509 differentially expressed genes (DEGs) were identified. Among them, 1,001 genes are up-regulated and 508 genes are down-regulated in P50 individuals compared with H9 individuals. The enrichment of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) of DEGs confirmed that many DEGs were associated with "Amino acid transport and metabolism", "Nucleotide transport and metabolism", and "Inorganic ion transport and metabolism", 25 of the DEGs related to the "ECM-receptor interaction passway", "sphingolipid metabolism passway", and "amino sugar and nucleotide sugar metabolism passway" were potentially involved in the process of CG development and mucus secretion. According to these data, we hypothesized that CG play an important role in providing favorable physiological environment for the glue secretion formation. In addition, GO enrichment and differential expression analysis of the DEGs in the CG indicate that this gland may be involved in the transporting of small solutes such as sugars, ions, amino acids and nucleotide sugar to the CG. Our findings lay the foundation for further research on CG function.

Transgenic characterization of two silkworm tissue-specific promoters in the haemocyte plasmatocyte cells

Haemocytes play crucial roles in insect metabolism, metamorphosis, and innate immunity. As a model of lepidopteran insects, the silkworm is a useful model to study the functions of both haematopoiesis and haemocytes. Tissue-specific promoters are excellent tools for genetic manipulation and are widely used in fundamental biological research. Herein, two haemocyte-specific genes, Integrin β2 and Integrin β3, were confirmed. Promoter activities of Integrin β2 and Integrin β3 were evaluated by genetic manipulation. Quantitative real-time PCR and western blotting suggested that both promoters can drive enhanced green fluorescent protein (EGFP) specifically expressed in haemocytes. Further evidence clearly demonstrated that the transgenic silkworm exhibited a high level of EGFP signal in plasmatocytes, but not in other detected haemocyte types. Moreover, EGFP fluorescence signals were observed in the haematopoietic organ of both transgenic strains. Thus, two promoters that enable plasmatocytes to express genes of interest were confirmed in our study. It is expected that the results of this study will facilitate advances in our understanding of insect haematopoiesis and immunity in the silkworm, Bombyx mori.

Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori

The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO) analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.

Genome-wide identification and analysis of elongase of very long chain fatty acid genes in the silkworm, Bombyx mori

Very long chain fatty acids (VLCFAs), such as sphingolipids, are components of cellular lipids, which are essential for cell proliferation. Mutations in the genes that encode proteins participating in VLCFA biosynthesis may cause inherited diseases, such as macular degeneration. Elongases of very long chain fatty acid (ELOVL) are enzymes that are involved in the biosynthesis of VLCFAs. Here, a total of 13 ELOVL genes, distributed across three chromosomes, were identified in the silkworm genome; all the ELOVL members contain a distinct ELO domain and a conserved HXXHH motif. Phylogenetic reconstruction was performed to analyze the evolutionary relationships among different species and to predict gene functions. The 13 ELOVL genes were assigned to the ELOVL3/6, ELOVL1/7, and ELOVL4 clades. Microarray and semiquantitative PCR analyses indicated that these genes are differentially expressed among various tissues, in turn suggesting functional divergence in the growth and development of each tissue. Further investigation showed that the expression level of the BGIBMGA000424 gene is significantly negatively correlated with the cocoon-shell weight among different silkworm strains. Taken together, the present study is the first comprehensive analysis of ELOVL genes in silkworm, and the results may serve as a foundation for further analysis of the physiological functions of ELOVL genes in silkworm.

Genome-Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori

WD40 proteins are scaffolding molecules in protein-protein interactions and play crucial roles in fundamental biological processes. Genome-wide characterization of WD40 proteins in animals has been conducted solely in humans. We retrieved 172 WD40 protein genes in silkworm (BmWD40s) and identified these genes in 7 other insects, 9 vertebrates and 5 nematodes. Comparative analysis revealed that the WD40 protein gene family underwent lineage-specific expansions during animal evolution, but did not undergo significant expansion during insect evolution. The BmWD40s were categorized into five clusters and 12 classes according to the phylogenetic classification and their domain architectures, respectively. Sequence analyses indicated that tandem and segmental duplication played minor roles in producing the current number of BmWD40s, and domain recombination events of multi-domain BmWD40s might have occurred mainly after gene duplication events. Gene Ontology (GO) analysis revealed that a higher proportion of BmWD40s was involved in processes, such as binding, transcription-regulation and cellular component biogenesis, compared to all silkworm genes annotated in GO. Microarray-based analysis demonstrated that many BmWD40s had tissue-specific expression and exhibited high and/or sex-related expression during metamorphosis. These findings contribute to a better understanding of the evolution of the animal WD40 protein family and assist the study of the functions of BmWD40s.